Deep image-to-image network learning for medical image analysis

ABSTRACT

A method and apparatus for automatically performing medical image analysis tasks using deep image-to-image network (DI2IN) learning. An input medical image of a patient is received. An output image that provides a result of a target medical image analysis task on the input medical image is automatically generated using a trained deep image-to-image network (DI2IN). The trained DI2IN uses a conditional random field (CRF) energy function to estimate the output image based on the input medical image and uses a trained deep learning network to model unary and pairwise terms of the CRF energy function. The DI2IN may be trained on an image with multiple resolutions. The input image may be split into multiple parts and a separate DI2IN may be trained for each part. Furthermore, the multi-scale and multi-part schemes can be combined to train a multi-scale multi-part DI2IN.

This application claims the benefit of U.S. Provisional Application No.62/276,309, filed Jan. 8, 2016, the disclosure of which is hereinincorporated by reference.

BACKGROUND OF THE INVENTION

The present invention relates to automated analysis of medical images,and more particularly, to automating various medical image analysistasks using deep image-to-image network learning.

Medical image analysis involves solving important tasks such as landmarkdetection, anatomy detection, anatomy segmentation, lesion detection,segmentation and characterization, cross-modality image registration,image denoising, cross-domain image synthesis, etc. Computer-basedautomation of these medical image analysis tasks brings significantbenefits to medical imaging. For example, one such benefit of automatingmedical image analysis tasks is that it allows structured image readingand reporting for a streamlined workflow, thereby improving imagereading outcomes in terms of accuracy, reproducibility, and efficiency.Other benefits of automatic medical image analysis tasks includeenabling personalized scanning at a reduced radiation dose, savingexamination time and cost, and increasing consistency andreproducibility of the examination.

Currently the technical approaches for various medical image analysistasks are task-dependent. In other words, for each task among landmarkdetection, anatomy detection, anatomy segmentation, lesion detection,segmentation and characterization, cross modality image registration,image denoising, cross-domain image synthesis, etc., there are amultitude of technical approaches crafted for such a task. Consequently,the approaches for solving the same task are very diverse in nature.There is no systematic, universal approach to address all of thesemedical image analysis tasks.

BRIEF SUMMARY OF THE INVENTION

The present invention provides a method and system for automaticallyperforming a medical image analysis task on an input image using deepimage-to-image network learning. Embodiments of the present inventionutilize a deep image-to-image network (DI2IN) learning framework tounify many different medical image analysis tasks. Embodiments of thepresent invention formulate various medical image analysis tasks as animage-to-image mapping problem, in which a trained DI2IN is used to mapan input medical image or cohort of input medical images to an outputimage that provides a result of a particular medical image analysistask.

In one embodiment of the present invention, an input medical image of apatient is received. An output image that provides a result of a targetmedical image analysis task on the input medical image is automaticallygenerated using a trained deep image-to-image network (DI2IN), Thetrained DI2IN uses a conditional random field (CRF) energy function toestimate the output image based on the input medical image and uses atrained deep learning network to model unary and pairwise terms of theCRF energy function.

These and other advantages of the invention will be apparent to those ofordinary skill in the art by reference to the following detaileddescription and the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a method for automatically performing a medical imageanalysis task using deep image-to-image network (DI2IN) learningaccording to an embodiment of the present invention;

FIG. 2 illustrates training a DI2IN using a deep learning model in aConditional Random Field (CRF) framework according to an embodiment ofthe present invention;

FIG. 3 illustrates a method of anatomical object segmentation in amedical image using a multiscale part-based DI2IN according to anembodiment of the present invention;

FIG. 4 illustrates an exemplary multiscale part-based DI2IN foranatomical object segmentation in a medical image according to anembodiment of the present invention;

FIG. 5 illustrates exemplary liver segmentation using the multi-scalepart-based DI2IN of FIG. 4; and

FIG. 6 is a high-level block diagram of a computer capable ofimplementing the present invention.

DETAILED DESCRIPTION

The present invention relates to a method and system for automaticallyperforming medical image analysis tasks using deep image-to-imagenetwork (DI2IN) learning. Embodiments of the present invention aredescribed herein to give a visual understanding of the medical imagedeep image-to-image network (DI2IN) learning method and the medicalimage analysis tasks. A digital image is often composed of digitalrepresentations of one or more objects (or shapes). The digitalrepresentation of an object is often described herein in terms ofidentifying and manipulating the objects. Such manipulations are virtualmanipulations accomplished in the memory or other circuitry/hardware ofa computer system. Accordingly, is to be understood that embodiments ofthe present invention may be performed within a computer system usingdata stored within the computer system.

Embodiments of the present invention utilize a deep image-to-imagenetwork (DI2IN) learning framework to unify many different medical imageanalysis tasks. Embodiments of the present invention can be used toautomatically implement various medical image analysis tasks, includinglandmark detection, anatomy detection, anatomy segmentation, lesiondetection, segmentation and characterization, cross-modality imageregistration, image denoising, cross-domain image synthesis, andquantitative parameter mapping. Embodiments of the present inventionformulate various medical image analysis tasks as an image-to-imagemapping problem, in which a DI2IN is trained to learn a mapping from aparticular type of input medical image or images to an output image thatprovides a result of a particular medical image analysis task.Embodiments of the present invention can be used to automaticallyperform any medical image analysis task for which the result ofperforming the medical image analysis task can be defined as an outputimage or images.

FIG. 1 illustrates a method for automatically performing a medical imageanalysis task using deep image-to-image network (DI2IN) learningaccording to an embodiment of the present invention. The method of FIG.1 includes a training stage 100 and a testing stage 110. The trainingstage 100, which includes steps 102-108, is performed off-line to traina DI2IN for a particular medical image analysis task. The testing stage110, which includes steps 112-116, performs the medical image analysistask on a newly input medical image using the trained DI2IN resultingfrom the training stage 100. Once the DI2IN for a particular medicalimage analysis task is trained in the training stage 100, the testingstage 110 can be repeated for each newly received input medical image(s)to perform the medical image analysis task on each newly received inputmedical image(s) using the trained DI2IN.

At step 102, an output image is defined for the medical image analysistask. The DI2IN learning framework described herein utilizes animage-to-image framework in which an input medical image or multipleinput medical images is/are mapped to an output image that provides theresult of a particular medical image analysis task. In the DI2INlearning framework, the input is an image I or a set of images I₁, I₂, .. . , I_(N) and the output will be an image J or a set of images J₁, J₂,. . . , J_(M). An image I includes a set of pixels (for a 2D image) orvoxels (for a 3D image) that form a rectangular lattice Ω={x} (x is a 2Dvector for a 2D image and a 3D vector for a 3D image) and defines amapping function from the lattice to a desired set, i.e., {I(x)εR; xεΩ}for a gray-value image or {I(x)εR³; xεΩ} for a color image. If a set ofimages are used as the input, then they share the same lattice Ω; thatis, they have the same size. For the output image J, its size is oftenthe same as that of the input image I, though different lattice sizescan be handled too as long as there is a defined correspondence betweenthe lattice of the input image and the lattice of the output image. Asused herein, unless otherwise specified, a set of images I₁, I₂, . . . ,I_(N) will be treated as one image with multiple channels, that is{I(x)εR^(N); xεΩ} for N gray images or {I(x)εR³ xεΩ} for N color images.

The DI2IN image-to-image framework can be used to formulate manydifferent medical image analysis problems. In order to use the DI2INframework to perform a particular medical image analysis task, an outputimage must be defined for the particular medical image analysis task.The solutions/results for many image analysis tasks are often notimages. For example, anatomical landmark detection tasks typicallyprovide coordinates of a landmark location in the input image andanatomy detection tasks typically provide a pose (e.g., position,orientation, and scale) of a bounding box surrounding an anatomicalobject of interest in the input image. According to an embodiment of thepresent invention, an output image is defined for a particular medicalimage analysis task that provides the result of that medical imageanalysis task in the form of an image. In one possible implementation,the output image for a target medical image analysis task can beautomatically defined, for example by selecting a stored predeterminedoutput image format corresponding to the target medical image analysistask. In another possible implementation, user input can be receivedcorresponding to an output image format defined by a user for a targetmedical image analysis task. Examples of output image definitions forvarious medical image analysis tasks are described below.

In an exemplary embodiment, the method of FIG. 1 can be used to performlandmark detection in an input medical image. Given an input medicalimage I, the task is to provide the exact location(s) of a singlelandmark or multiple landmarks of interest {x₁, I=1,2, . . . }. In oneimplementation, the output image J can be defined as:J(x)=Σ_(l)Σ_(i) *g(|x−x _(l)|;σ),  (1)where δ is a delta function. This results in a mask image in which pixellocations of the landmark l have a value of l, and all other pixellocations have a value of zero. In an alternative implementation, theoutput image for a landmark detection task can be defined as an imagewith a Gaussian-like circle (for 2D image) or ball (for 3D image)surrounding each landmark. Such an output image can be defined as:J(x)=Σ_(l)Σ_(i) *g(|x−x _(l)|;σ)  (2)where g(t) is a Gaussian function with support σ and |x−x_(l)| measuresthe distance from the pixel x to the l^(th) landmark.

In an exemplary embodiment, the method of FIG. 1 can be used to performanatomy detection in an input medical image. Given an input image I, thetask is to find the exact bounding box of an anatomy of interest (e.g.,organ, bone structure, or other anatomical object of interest). Thebounding box B(θ) can be parameterized by θ. For example, for anaxis-aligned box, θ=[x_(c),s], where x_(c) is the center of the box ands is the size of the box. For a non-axis-aligned box, θ can includeposition, orientation, and scale parameters. The output image J can bedefined as:J(x)=1 if xεB(θ); otherwise 0.  (3)This results in a binary mask with pixels (or voxels) equal to 1 withinthe bounding box and equal 0 at all other pixel locations. Similarly,this definition can be extended to cope with multiple instances of asingle anatomy and/or multiple detected anatomies.

In an exemplary embodiment, the method of FIG. 1 can be used to performanatomy segmentation in an input medical image. Given an input image I,the task is to find the exact boundary of an anatomy or anatomies ofinterest. In one implementation, the output image J can be a multi-labelmask function, defined as:J(x)=1 if xεAnatomy_(l); otherwise 0.  (4)

In an alternative implementation, the output image J can be defined asan image having a Guassian-like band surrounding the boundary of eachsegmented anatomy of interest. Such an output image can be defined as:J(x)=g(d(x,Anatomy_(l) boundary)),  (5)where d(x, Anatomy_(l) boundary) is the distance from the pixel x to theboundary of the l^(th) segmented anatomy. In other possibleimplementations, representations such as a signed distance function oreven level sets may also be used to define the output image for theanatomy segmentation task.

In an exemplary embodiment, the method of FIG. 1 can be used to performlesion detection, segmentation, and characterization in an input medicalimage. In lesion detection and segmentation, given an input image I, thetasks are to detect and segment one or multiple lesions. The outputimage J for lesion detection and segmentation can be defined asdescribed above for the anatomy detection and segmentation tasks. Tohandle lesion characterization, which aims to distinguish if a lesion isbenign or malignant, if a liver lesion is hyperdense or hypodense, etc.,the output image J can be defined by further assigning new labels in themulti-label mask function (Eq. (4)) or the Gaussian band (Eq. (5)) sothat fine-grained characterization labels can be captured in the outputimage.

In an exemplary embodiment, the method of FIG. 1 can be used to performimage denoising of an input medical image. Given an input image I, theimage denoising task generates an output image J in which the noise isreduced.

In an exemplary embodiment, the method of FIG. 1 can be used to performcross-domain image synthesis. Given an input image I acquired from asource domain, the cross-domain image synthesis task generates an outputimage J as if it was acquired from a target domain. Examples ofsource/target domains for cross-domain image synthesis includes, but isnot limited to, computed tomography (CT)/magnetic resonance (MR),T1-weighted MR (MRT1)/T-2 weighted MR (MRT2), CT/DynaCT, etc.

In an exemplary embodiment, the method of FIG. 1 can be used to performcross-modality image registration. Given a pair of input images {I₁,I₂},the image registration task finds a deformation field d(x) such thatI₁(x) and I₂(x−d(x)) are in correspondence. In an advantageousimplementation, the output image J(x) is exactly the deformation field,J(x)=d(x).

In an exemplary embodiment, the method of FIG. 1 can be used to performquantitative parametric mapping. Given a set of input images {I₁, . . ., I_(n)} and a pointwise generative model {I₁, . . . , I_(n)}(X)=F(J₁, .. . J_(m).)(X), a parametric mapping task aims to recover thequantitative parameters that generated the input images. Examples ofquantitative mapping tasks include MR fingerprinting and materialdecomposition from spectral CT.

It is to be understood, that for any medical image analysis task, aslong as an output image can be defined for that medical image analysistask that provides the results of that medical image analysis task, themedical image analysis task can be regarded as a DI2IN learning problemand performed using the method of FIG. 1.

Returning to FIG. 1, at step 104, input training images are received.The input training images are medical images acquired using any type ofmedical imaging modality, such as computed tomography (CT), magneticresonance (MR), DynaCT, ultrasound, x-ray, positron emission tomography(PET), etc. The input training images correspond to a particular medicalimage analysis task for which the DI2IN is to be trained. Depending onthe particular medical image analysis task for which the DI2IN is to betrained, each input training image for training the DI2IN can be anindividual medical image or a set of multiple medical images. The inputtraining images can be received by loading a number of previously storedmedical images from a database of medical images.

At step 106, output training images corresponding to the input trainingimages are received or generated. The DI2IN trained for the particularmedical image analysis task is trained based on paired input and outputtraining samples. Accordingly for each input training image (or set ofinput training images), a corresponding output training image isreceived or generated. The output images for various medical imageanalysis tasks are defined as described above in step 102. In someembodiments, the output images corresponding to the input trainingimages may be existing images that are stored in a database. In thiscase, the output training images are received by loading the previouslystored output image corresponding to each input training image. In thiscase, the output training images may be received at the same time as theinput training images are received. For example, for the image denoisingtask, a previously stored reduced noise medical image corresponding toeach input training image may be received. For the cross-domain imagesynthesis task, each input training image is a source domain medicalimage and a previously acquired target domain medical imagecorresponding to each source domain medical image may be received. Forthe cross-modality image registration task, for each input trainingimage pair, a previously stored deformation field defining aregistration between the input training image pair may be received. Forthe quantitative parametric mapping task, for each set of input trainingimages, a previously acquired set of quantitative parameters can bereceived. For landmark detection, anatomy detection, anatomysegmentation, and lesion detection, segmentation and characterizationtasks, if previously stored output images (as defined above) exist forthe input training images, the previously stored output images can bereceived.

In other embodiments, output training images can be generatedautomatically or semi-automatically from the received input trainingimages. For example, for landmark detection, anatomy detection, anatomysegmentation, and lesion detection, segmentation and characterizationtasks, the received input training images may include annotateddetection/segmentation/characterization results or manual annotations oflandmark/anatomy/lesion locations, boundaries, and/or characterizationsmay be received from a user via a user input device (e.g., mouse,touchscreen, etc.). The output training images can then be generated byautomatically generating a mask images or Gaussian-like circle/bandimage as described above for each input training image based on theannotations in each input training image. It is also possible, that thelocations, boundaries, and/or characterizations in the training inputimages be determined using an existing automatic or semi-automaticdetection/segmentation/characterization algorithm and then used as basisfor automatically generating the corresponding output training images.For the image denoising task, if no reduced noise images correspondingto the input training images are already stored, an existing filteringor denoising algorithm can be applied to the input training images togenerate the output training images. For the cross-modality imageregistration task, the output training images can be generated byregistering each input training image pair using an existing imageregistration algorithm to generate a deformation field for each inputtraining image pair. For the quantitative parametric mapping task, theoutput training image can be generated by applying an existingparametric mapping algorithm to each set of input training images tocalculate a corresponding set of quantitative parameters for each set ofinput training images.

At step 108, a deep image-to-image network (DI2IN) is trained for aparticular medical image analysis task based on the input and outputtraining images. According to an advantageous embodiment of the presentinvention, a mathematical model for the DI2IN is based on a ConditionalRandom Field (CRF), in which an energy function E is defined as:E(J(x)|I(x);θ)=Σ_(xEΩ) U(J(x)|I(x);θ)+E _(x,yεΘ)V(J(x),J(y)|I(x)I(y);θ),  (6)where U(J(x)I|(x)) is the unary term, V(J(x),J(y)|I(x),I(y)) is thepairwise term, Θ is the set of neighboring pixels, and θ is the modelingparameter. The likelihood is now given by:P(J(x)|I(x);θ)=exp(−E(J(x)|I(x);θ))/Z(I(x);θ),  (7)where Z(I(x); θ) is a normalizing partition function.

During training, assuming the availability of paired training datasets{(I_(n)(x),J_(n)(x)); n=1,2, . . . }, following the maximum likelihoodprinciple, the goal of the training is maximize the likelihood P withrespect to the modeling parameter θ:min_(θ)Σ_(n) [E(J _(n)(x)|I _(n)(x);θ)+log Z(I(x);θ)].  (8)In some possible implementations, a regularization term may also beincluded in Equation (8) to capture a prior belief about the parameterθ. Choices of the regularization include L2 norm, sparsity, etc. Thetraining learns the modeling parameter θ that maximizes the likelihoodP. During the testing (or estimation/inference) stage (110 of FIG. 1),given an newly received input image I(x), an output image is generatedthat maximizes the likelihood P(J(x)I|(x); θ) with the parameter θ fixedas the parameter learned during training.

The modeling choices for the unary and pairwise terms of the CRF energyfunction largely determines the effectiveness of the solution. Accordingto an advantageous embodiment of the present invention, deep learning isused to model the unary and pairwise terms of the CRF energy function.FIG. 2 illustrates training a DI2IN using a deep learning model in aConditional Random Field (CRF) framework according to an embodiment ofthe present invention. As shown in FIG. 2, a deep network 200 is learnedto model the unary and pairwise terms of the CRF energy function. A deepnetwork 200 includes an input layer 202, multiple hidden layers 204, andan output layer 206. For example, the deep network 200 may be a fullyconnected deep neural network or a convolutional neural network (CNN).The connections between two consecutive layers k and k−1 in the deepneural network 200 are through a set of weights or a weight matrixW_(k,k-1). The input layer 202 of the deep network 200 corresponds toimage data of the input image (or input images). The output layer 206 ofthe deep network has two nodes, one which outputs a value for the unaryterm of the CRF energy function, and one which outputs the pairwise termof the CRF energy function. The outputs from the nodes of the outputlayer 206 of the deep network 200 are then directly connected into theCRF energy function. The parameters for the deep network 200 areθ={W_(k,k-1,)k=2,3, . . . }. Accordingly, in order to train the DI2IN,given paired input and output training images, weights for all thelayers of the deep network 200 are learned which result in unary andpairwise terms of the CRF energy function which maximize the likelihoodP(J(x)|I(x); θ). Alternatively, the deep network can be trained togenerate the unary term of the CRF energy function and the pairwise termcan be trained or defined using other methods.

In an embodiment in which the desired output image is a multi-labelmask, for example in the cases of landmark detection, anatomy detectionand segmentation, and lesion detection, segmentation, andcharacterization, a multi-class classifier can be learned via a deepnetwork that computes the probability P(l|I(x); θ) of assigning theimage pixel I(x) with label l and the unary term can be set as:U(J(x)=1(x);θ)=−log(P(l|I(x);θ)).  (9)For the pairwise term, it is advantageous to enforce label smoothness orcross-label context. If the image content at locations x and y areclose, their labels should be close as well. In a possibleimplementation, to enforce label smoothness, the pairwise term can beset as:V(J(x)=l,I(y)=m|I(x),I(y);θ)=δ(l−m)G(I(x),I(y)),  (10)where g (I(x),I(y)) measures the closeness between I(x) and I(y) interms of both spatial locations and feature values. Alternatively, toleverage cross-label context, a deep network can be trained too, inwhich paired class labels (l, m) are used. In other words, the deepnetwork P(l, m|I(x),I(y),θ) is learned to classify (I(x),I(y)) into oneof the paired classed (l, m). In this case, the pairwise term can be setas:V(J(x)=l,J(y)=m|I(x),I(y);θ)=log(l,m|I(x),I(y)).  (11)

In an embodiment in which the output image is a real-valued image, forexample in the case of image synthesis, image denoising, and imageregistration, etc., a regression function F (I(x); θ) can be learned viaa deep network that approximates the target output image J(x) and theunary term can be set as:

$\begin{matrix}{{{U\left( {{\left. {J(x)} \middle| {I(x)} \right.;\theta},\sigma} \right)} = {\frac{{{{J(x)} - {F\left( {{I(x)};\theta} \right)}}}^{2}}{\left( {2\sigma^{2}} \right)} + {\log(\sigma)}}},} & (12)\end{matrix}$where σ is a pre-specified standard deviation value. For the pairwiseterm, to enforce smoothness in the spatial locations, the predictedoutput values, and the input values, the pairwise term can be set as:V(J(x),J(y)|I(x),I(y);θ)=λ₁ ∥J(x)−J(y)∥²+λ₂ ∥J(x)−I(y)∥²+λ₃ ∥x−y∥²,  (13)where λ₁, λ₂, and λ₃ are weighting parameters used to weight therelative importance of smoothness in the predicted output values, theinput values, and the spatial locations, respectively. Alternatively, itis possible to learn a joint regression function G that predicts bothvalues of (J(x),J(y))=G(I(x),I(y); θ) based on U(x) and I(y) and thenset the pairwise term as:

$\begin{matrix}{{{U\left( {{J(x)},\left. {J(y)} \middle| {I(x)} \right.,{{I(y)};\theta}} \right)} = {\frac{{{\left\lbrack {{J(x)},{J(y)}} \right\rbrack - {G\left( {{I(x)},{{I(y)};\theta}} \right)}}}^{2}}{\left( {2\rho^{2}} \right)} + {\log(\rho)}}},} & (14)\end{matrix}$where σ is a pre-specified standard deviation value.

In another possible implementation, where the target real-valued image.J is the same for all input image I, but unknown, the training can beextended through the iteration of 2 steps: first, the energy functioncan be optimized with a given target output image J_(t), and second thebest target output image J_(t+1) can be learned given the optimizedenergy function. For example, this can be applied to groupwise imageregistration or atlas-based image registration.

During learning (training), the deep-network is trained in an end-to-endfashion such that Equation (8) is minimized by using the deep networkmodel parameters (i.e., the weights of the deep network). This isperformed by computing the gradient of the CRF energy function withrespect to the deep network model parameters, which can be done byapplying the well-known chain rule. As a result, the well-known BackPropagation (BP) algorithm can be used to implement stochastic gradientdescent in order to learn the deep network model parameters (weights)that minimize Equation (8). In the testing stage, the deep network withthe learned weights is then used to calculate the unary and pairwiseterms of the CRF energy function and the output image is found thatoptimizes the CRF energy function (i.e., minimizes Equation (8)). Tohandle complexity in the CRF inference, the mean field approximationmethod can be utilized to derive a solution efficiently. In anadvantageous implementation, to reduce overfitting in learning the deepnetwork, a convolution network, such as a CNN, in which a reduced numberof parameters is defined across two consecutive layers of the deepnetwork. When the convolutional network is used for every pixellocation, a fully convolutional network is implied.

Returning to FIG. 1, in the testing stage 110, at step 112, an inputmedical image is received. The input medical image can be a 2D or 3Dmedical image acquired using any type of medical imaging modality, suchas CT, MR, DynaCT, ultrasound, PET, etc. Depending on the medicalimaging task to be performed for the received input medical image, theinput medical image may be a set of medical images. The input medicalimage may be received directly from an image acquisition device used toacquire the input medical image, such as a CT scanner, MR scanner, etc.Alternatively, the input medical image may be received by loading apreviously acquired medical image from a storage or memory of a computersystem or receiving a medical image that has been transmitted from aremote computer system.

At step 114, an output image that provides a result of a medical imageanalysis task is generated from the input image using the trained deepimage-to-image network (DI2IN). As described above, the trained DI2INincludes a trained deep network that calculates a unary term and apairwise term of the CRF energy function for a predicted output imagebased on the input medical image and the learned weights of the deepnetwork. The output image is generated by estimating an output imagethat optimizes the CRF energy function. In particular, with the deepnetwork parameters fixed using the learned weights, an output image isfound that minimizes Equation (8) (i.e., maximizes the likelihood of theCRF energy function) for the received input image. The unary andpairwise terms calculated using the trained deep network are set basedon the type of output image to be generated, as described above inconnection with step 108. The type of output image generated for thetarget medical image task to be performed is defined at step 102 of thetraining stage 100 and various examples are described above. Forexample, a multi-label or binary mask image or a Gaussian-like circle orband image can be generated to provide the results of a landmarkdetection, anatomy detection or segmentation, or lesion detection,segmentation and characterization task. A denoised medical image can begenerated to provide the result of an image denoising task. Asynthesized target domain medical image may be generated based on aninput source domain medical image to provide the result on across-domain image synthesis task. A deformation field may be generatedto provide the result for a cross-modality image registration taskbetween a pair of input medical images. An image map of quantitativeparameters may be generated from a set of input medical images toprovide the result of a parametric mapping.

At step 116, the generated output image, which provides the result ofthe target medical image analysis task for the input image, is output.For example, the generated output image can be output by displaying thegenerated output image on a display device of a computer system. Thegenerated output image can also be output by storing the generatedoutput image on a memory or storage of a computer system or bytransmitting the generated output image to a remote computer system.

According to an advantageous embodiment of the present invention, amultiscale part-based DI2IN can be trained and used to improveefficiency, robustness, and accuracy of a medical image analysis task.In the present disclosure, a multiscale part-based DI2IN is describedfor anatomical object segmentation in a 3D medical image. It is to beunderstood that such a multiscale part-based DI2IN can be trained andapplied for other medical image analysis tasks as well.

Automatic detection and segmentation of an anatomical structure (object)in medical images is often a prerequisite for subsequent tasks such asrecognition, measurement, or motion tracking, and therefore has numerousapplications. Various methods have been proposed for medical imagesegmentation. However, the robustness and accuracy of those methodsstill needs further improvement on challenging segmentation problemswhere the target object exhibits high variations in position,orientations, size, shape, appearance, etc. Recently, fullyconvolutional network (FCN) has been proposed to leverage a deepconvolutional neural network to perform segmentation with one-shot pixelclassification (i.e., no bounding box detection is required) in 2Dimages. The network is trained end-to-end and the segmentation procedureis relatively efficient using a graphics processing unit (GPU) card.However, in FCN, voxel classification is based on a fixed field-of-view(FoV), which may not be optimal, especially for objects exhibiting largevariations in size. With the rapid progress of medical imagingtechnology in the past decade, most medical images are 3D in nature(e.g., CT, MR, or ultrasound). Extending FCN to 3D bring severalpractical issues, including increased computational cost and memoryfootprint.

In an advantageous embodiment of the present invention, a multiscalepart-based DI2IN is used for anatomical object segmentation of 3Dmedical images in order to address the above described challenges. Ascale space representation (i.e., an image pyramid) of the input imagedata at multiple image resolutions can be built. For example, reducedresolution images of an input image at resolutions of 16 mm, 8 mm, 4 mm,and 2 mm can be generated. Such an image pyramid can be used in variousways during training and testing. One possible approach is to extractimage patches at multiple resolutions. All of these image patches canthen be used to simultaneously perform classification. A patch with afixed size actually has a different field of view (FoV) at differentresolutions. For example, a patch with 15×15×15 voxels has an FoV of240×240×240 mm³ at the 16 mm resolution. Joint training with patchesfrom multiple resolutions can increase robustness of the trainedclassifier under variation of the object size. As long as the objectsize matches one of the FoVs, it can be potentially segmented correctly.However, such an approach cannot accelerate the segmentation speed orreduce the memory footprint.

Alternatively, in an advantageous embodiment of the present invention, asequence of DI2IN classifiers are trained on images with differentresolutions. This results in a multiscale DI2IN including a respectiveDI2IN classifier for each of a plurality of resolutions, in which thesegmentation result at a lower resolution is used to constrain the voxelclassification at a higher resolution. This can significantly increasethe segmentation speed and reduce the memory footprint required for thesegmentation. In addition, a part-based DI2IN can be utilized forsegmentation of an input image, in which the input image data is splitinto multiple parts and a separate trained DI2IN classifier is used toperform the segmentation in each of the parts of the input image. Thiscan improve efficiency and accuracy of the segmentation. In variouspossible implementations, either multiscale DI2IN or part-based DI2INmay be independently implemented or may be combined into a multiscalepart-based DI2IN.

FIG. 3 illustrates a method of anatomical object segmentation in amedical image using a multiscale part-based DI2IN according to anembodiment of the present invention. At step 302, an input medical imageis received. The input medical image can be a medical image acquiredusing any type of medical imaging modality, such as CT, MR, ultrasound,PET, DynaCT, x-ray, etc. In an advantageous implementation, the inputmedical image is a 3D medical image, but the present invention is notlimited thereto. The input medical image may be received directly froman image acquisitions device, such as a CT scanner, MR scanner, etc.Alternatively, the input medical image may be received by loading apreviously acquired medical image from a storage or memory of a computersystem or receiving a medical image that has been transmitted from aremote computer system.

At step 304, an image pyramid with multiple reduced resolution images ofthe input medical image is generated. The image pyramid is a scale spacerepresentation of the input medical image at multiple resolutions. Forexample, reduced resolution images of the input medical image atresolutions of 16 mm, 8 mm, 4 mm, and 2 mm can be generated. The numberand resolutions of the reduced resolution images that are generatedcorrespond to the structure of a trained multiscale part-based DI2IN(see step 306), which can be set in training of the multiscalepart-based DI2IN. The image pyramid of the input medical image can begenerated using well known techniques for generated reduced resolutionimages of an input image.

At step 306, a target anatomical object is segmented in each of thereduced resolution images using a sequence of trained DI2IN classifiers.The multiscale part-based DI2IN includes a respective trained DI2IN foreach of a plurality of resolution levels. Each respective DI2IN istrained as described above using the method of FIG. 1. Accordingly, eachtrained DI2IN generates an output image that provides segmentationresults for the target anatomical object at the respective resolutionlevel. The segmentation result from the respective trained DI2IN at eachreduced resolution level is used to constrain the voxel classification(segmentation) at the subsequent higher resolution level. For example,the higher level DI2IN classification can be constrained to asegmentation mask generated at a lower resolution. That is, therespective trained DI2IN at each reduced resolution level can generate asegmentation mask, and the segmentation mask at each reduced resolutionlevel can be used to define a region of interest (ROI) in the image atthe next higher resolution. The ROI is then cropped from the higherresolution image and used as the input image to the next trained DI2INin the classifier. The ROI in a higher resolution image can correspondto voxels in the lower resolution segmentation mask having non-zerovalues. In a possible embodiment, the coarse segmentation mask from thelower resolution image may be expanded to compensate for segmentationerror due to partial volume effects or imaging noise prior to definingthe ROI in the higher resolution image. In many cases, the segmentationresult at low resolutions will only occupy a small portion of the imagedata, such as 10% or even as low as 1%. Therefore, the classification(segmentation) result at low resolutions can be used to eliminate alarge portion of the data for consideration at higher resolutions, whichsignificantly increases segmentation speed.

In Convolutional Neural Networks (CNN), convolution of filters isperformed to extract image features. The filter responses are cached asinput to the next CNN layer. If the network is deep or many filters(e.g., hundreds of filters) are used at a certain layer, the memoryfootprint is high. The maximum amount of memory of a single GPUcurrently available on market is 12 GB, e.g., the widely used NVIDIA GTXTitan X GPU. (NVIDIA Tesla K80 has 24 GB memory, but it combines two K40GPUs and there is overhead in transferring data between GPUs.) A typicalfull-body CT scan contains about 512×512×1000 voxels. Represented with a“float” precision (4 bytes), such a CT scan consumes about 1 GB memory.With 12 GB memory, we can only have up to 12 filters at the originalhigh resolution. In reality, the possible number of filters is evensmaller since other CNN layers also consume memory. By using thesegmentation mask at a lower resolution on the image pyramid toconstrain the input image data at each subsequent higher resolution, alarge portion of the image can be discarded completely in the followingprocessing at the subsequent higher resolution. Instead of taking thewhole volume as input to the next (higher resolution) layer, the volumecan be cropped based on the ROI determined by the coarse segmentation ata lower resolution. In this way, the memory footprint is significantlyreduced during training and testing of the DI2IN.

FIG. 4 illustrates an exemplary multiscale part-based DI2IN foranatomical object segmentation in a medical image according to anembodiment of the present invention. As shown in FIG. 4, the multiscalepart-based DI2IN includes respective trained DI2INs 402, 404, and 406for reduced resolution levels of 8 mm, 4 mm, and 2 mm, respectively.Accordingly, reduced resolution images of the input medical image aregenerated with resolutions of 8 mm, 4 mm, and 2 mm. DI2IN 402 inputs the8 mm reduced resolution image and generates a segmentation maskproviding a segmentation result in the 8 mm reduced resolution image.The segmentation mask for the 8 mm reduced resolution image defines aROI which is cropped from the 4 mm reduced resolution image and input toDI2IN 404. DI2IN 404 generates a segmentation mask providing asegmentation result in the ROI of the 4 mm reduced resolution image, andthe 4 mm resolution segmentation mask defines a ROI which is croppedfrom the 2 mm reduced resolution image and input to DI2IN 406. DI2IN 406generates a segmentation mask providing a segmentation result in the ROIof the 2 mm reduced resolution image. The 2 mm resolution segmentationmask defines an ROI in the original resolution image, which is thenclassified using a part-based DI2IN.

In addition to reducing the computation time and memory footprint,multiscale DI2IN can also help to compensate variations in object poseand size, thereby increasing the segmentation accuracy. At a lowresolution, even though DI2IN may not be able to provide an accuratesegmentation of the target object, it will usually provide accurateinformation of the object location, orientation, and size. With acropped volume as input to the next level DI2IN, variation in the objectcenter can be removed by putting the object at the center of the croppedvolume. In addition, the cropped volume can be further normalized withrespect to estimated orientation and size. For example, the ROI can bealigned to the estimated orientation (a tilted ROI) and the ROI size canbe set to be proportional to the estimated object size. Once an ROI isdetermined, other normalization is also possible. For example,non-linear voxel intensity transformation can be performed to make theROI intensity histogram match statistics calculated from the trainingset. A classification probability map at a lower resolution can also beexploited as an additional input channel to the next DI2IN. This mayfurther increase the classification accuracy.

Returning to FIG. 3, at step 308, the original resolution image isdivided into multiple parts. At step 310, the anatomical object issegmented in each part using a respective trained DI2IN classifier. Thesegmentation of the original resolution input medical image can beconstrained based on the segmentation mask generated from the highestresolution reduced resolution image (e.g., 2 mm in FIG. 4). Inparticular, the segmentation mask generated from highest resolutionreduced resolution image can define an ROI in the original resolutionimage. The ROI can be cropped from the original resolution input medicalimage and used as the input image for segmentation at the originalresolution. However, if the target object is large, such as the lungs orliver, the cropped volume can still consume a large amount of memory atthe highest resolution. Even though DI2IN segments a whole input imagewith a single forward evaluation of the network, the FoV to performclassification for each voxel is much smaller and fixed. Therefore, theclassification of a voxel on a top portion of the object does not useinformation from the bottom portion of the object at all (if the objectheight is larger than the FoV. Thus, according to an advantageousembodiment of the present invention, a part-based approach can be usedto further reduce the memory footprint of the multiscale DI2IN.

In an advantageous implementation, the original resolution input imageresulting from cropping the ROI from the original resolution inputmedical image can be split into multiple overlapping regions, eachreferred to as a “part” of the image. According to an advantageousimplementation, neighboring regions (parts) should have an overlap atleast half of the FoV of the trained deep network in order to generateexactly the same output as performing classification on the whole inputimage. For example, if the neural network takes a patch of 15×15×15voxels as input for classification, the overlap between neighboringregions (parts) should be 8 voxels or more. A respective trained DI2INis trained for segmentation of the target anatomical object in each ofthe image parts and segmentation of the anatomical object isindependently performed in each of the parts of the input originalresolution image using the respective trained DI2IN classifier. Eachregion (part) needs to have a size at least as large as the FoV forvoxel classification. If the size of each region (part) is set to thesame size as the classification FoV, each voxel will have its ownregion. This is equivalent to patch-based classification, which is notefficient. Therefore, in an advantageous implementation, the image canbe split into a small number of regions (e.g., 5) having a size largerthan the classification FoV subject to the constraint of GPU memory. Theimage characteristics of each part and its surrounding tissue may bequite different. Therefore, a divide-and-conquer strategy can beexploited to train a respective DI2IN for each part. The can make thelearning problem easier, resulting in increased segmentation accuracy.The respective DI2IN for each part can be trained as described aboveusing the method of FIG. 1.

As shown in FIG. 4, the multiscale part-based DI2IN of FIG. 4 includesDI2INs 408, 410, 412, 414, and 416, each of which performs segmentationof a respective part of the input medical image at the originalresolution. The 2 mm segmentation mask generated by DI2IN 406 defines anROI that is cropped from the original resolution input medical image,resulting in a cropped original resolution image. The cropped originalresolution image is divided into the following five overlapping parts: atop-left part, a top-right part, a center part, a bottom-left part, anda bottom-right part. The size of these parts can be set during training.Each of the parts of the cropped resolution image is an input image thatis input to a respective trained DI2IN. DI2INs 408, 410, 412, 414, and416 segment that top-left part, top-right part, center part, bottom-leftpart, and bottom-right part, respectively. Each of the part-basedoriginal resolution DI2INs 408, 410, 412, 414, and 416 inputs therespective part of the cropped resolution image and outputs asegmentation mask that provides segmentation results for the prospectivepart. FIG. 5 illustrates exemplary liver segmentation using themulti-scale part-based DI2IN of FIG. 4. As shown in FIG. 5, image 502shows a full torso CT scan at 8 mm resolution. Image 504 shows a croppedliver ROI at the 4 mm resolution using the coarse segmentation at the 8mm resolution. Image 506 shows a cropped ROI at the 2 mm resolution.Images 508, 510, 512, 514, and 516 show cropped top-left, top-right,center, bottom-left, and bottom-right parts, respectively, of the ROI atthe original resolution.

In the embodiment described above in which multiscale and part-basedDI2IN are combined, the cropped original resolution image generated fromthe ROI defined based on the segmentation mask at the highest reducedresolution is divided into multiple parts and each part is independentlysegmented using a respective trained DI2IN. It is to be understood, thatpart-based DI2IN can also be applied without multiscale DI2IN, in whichcase the whole input medical image is divided into a plurality of partsand a respective trained DI2IN used to perform segmentation in eachpart.

Returning to FIG. 3, at step 312, the segmentation results from themultiple parts of the original resolution image are aggregated togenerate a final segmentation image. A respective output image, such asa segmentation mask, can be the respective DI2IN trained for each part,and the output images are combined to generate a final output image(e.g., segmentation mask) that provides the final segmentation result.Due to the overlap between neighboring regions (parts), voxels in theoverlapping areas have multiple outputs from different DI2INs. Dependingon the medical image analysis task, various aggregation methods can beused to combine the overlapping areas. If the output is a real valueimage, the values of the voxels in overlapping areas of output imagescan be averages, either using a weighted or unweighted average. Forsegmentation (or detection or characterization), the output for eachvoxel is a class label that is a discreet value from a limited set. Inthis case, majority voting (weighted or unweighted) can be used todetermine the voxel values in the final output image for voxels inoverlapping areas of the output images for the multiple parts.

At step 314, the final segmentation image is output. For example, thefinal segmentation image can be output by displaying the finalsegmentation image on a display device of a computer system. The finalsegmentation image can also be output by storing the final segmentationimage on a storage or memory of a computer system or by transmitting thefinal segmentation image to a remote computer system. In addition to thefinal segmentation image, the output images providing the segmentationresults at the various resolutions and/or for the various parts can alsobe output. For example, one or more of the output images from themultiscale and multi-part DI2INs can be displayed on the display device.

As described above in the method of FIG. 3, multiscale and part-basedDI2IN are used together. It is to be understood that either multiscaleDI2IN or part-based DI2IN may also be used independent of one another.The method of FIG. 3 uses multiscale part-based DI2IN to automaticallyperform anatomical object segmentation in a 3D medical image. It is tobe understood that this multiscale and/or part-based DI2IN framework canbe similarly applied to other medical image analysis tasks as well. Themultiscale and part-based DI2IN framework described for the anatomicalobject segmentation task can be applied straightforwardly to medicalimage analysis tasks that generate a mask image, such as landmarkdetection, anatomical object detection, and lesion detection,segmentation and characterization. The part-based DI2IN can also beapplied straightforwardly to other medical image analysis tasks, such asimage denoising, cross-domain image synthesis, cross-modality imageregistration, and quantitative parametric mapping. In an exemplaryimplementation, in order to apply multiscale DI2IN to medical imageanalysis tasks such as image denoising, cross-domain image synthesis,cross-modality image registration, and quantitative parametric mapping,output images can be generated at various resolution levels and theestimated output images at various resolution levels can be aggregated,for example by averaging or calculating a weight average of theestimated output images at the various resolution levels.

The above-described methods for training a DI2IN, automaticallyperforming a medical image analysis task using a DI2IN, and anatomicalobject segmentation in a medical image using a multiscale part-basedDI2IN may be implemented on a computer using well-known computerprocessors, memory units, storage devices, computer software, and othercomponents. A high-level block diagram of such a computer is illustratedin FIG. 6. Computer 602 contains a processor 604, which controls theoverall operation of the computer 602 by executing computer programinstructions which define such operation. The computer programinstructions may be stored in a storage device 612 (e.g., magnetic disk)and loaded into memory 610 when execution of the computer programinstructions is desired. Thus, the steps of the methods of FIGS. 1 and 3may be defined by the computer program instructions stored in the memory610 and/or storage 612 and controlled by the processor 604 executing thecomputer program instructions. An image acquisition device 620, such asan MR scanning device or a CT scanning device, can be connected to thecomputer 602 to input image data to the computer 602. It is possible toimplement the image acquisition device 620 and the computer 602 as onedevice. It is also possible that the image acquisition device 620 andthe computer 602 communicate wirelessly through a network. In a possibleembodiment, the computer 602 can be located remotely with respect to theimage acquisition device 620 and the method steps described herein canbe performed as part of a server or cloud based service. In this case,the method steps may be performed on a single computer or distributedbetween multiple networked computers. The computer 602 also includes oneor more network interfaces 606 for communicating with other devices viaa network. The computer 602 also includes other input/output devices 608that enable user interaction with the computer 602 (e.g., display,keyboard, mouse, speakers, buttons, etc.). Such input/output devices 608may be used in conjunction with a set of computer programs as anannotation tool to annotate volumes received from the image acquisitiondevice 620. One skilled in the art will recognize that an implementationof an actual computer could contain other components as well, and thatFIG. 6 is a high level representation of some of the components of sucha computer for illustrative purposes.

The foregoing Detailed Description is to be understood as being in everyrespect illustrative and exemplary, but not restrictive, and the scopeof the invention disclosed herein is not to be determined from theDetailed Description, but rather from the claims as interpretedaccording to the full breadth permitted by the patent laws. It is to beunderstood that the embodiments shown and described herein are onlyillustrative of the principles of the present invention and that variousmodifications may be implemented by those skilled in the art withoutdeparting from the scope and spirit of the invention. Those skilled inthe art could implement various other feature combinations withoutdeparting from the scope and spirit of the invention.

The invention claimed is:
 1. A method for automatically performing amedical image analysis task on a medical image of a patient, comprising:receiving an input medical image of a patient; and automaticallygenerating an output image that provides a result of a target medicalimage analysis task on the input medical image using a trained deepimage-to-image network (DI2IN), wherein the DI2IN uses a conditionalrandom field (CRF) energy function to estimate the output image based onthe input medical image and uses a trained deep learning network tomodel unary and pairwise terms of the CRF energy function, whereinautomatically generating the output image that provides the result ofthe target medical image analysis task on the input medical image usingthe DI2IN comprises: generating an image pyramid with a plurality ofreduced resolution images of the input medical image at an originalresolution; generating a respective output image that provides a resultof the target medical image analysis task on each of the reducedresolution images of the input medical image using a sequence of trainedDI2INs; dividing the input medical image at the original resolution intoa plurality of parts; generating a respective output image that providesa result of the target medical image analysis task on each of theplurality of parts of the original resolution input medical image usinga respective trained DI2IN for each of the plurality of parts; andaggregating the output images that provide the results of the targetmedical image analysis task on each of the plurality of parts togenerate a final output image that provides the result of the targetmedical image analysis task on the input medical image.
 2. The method ofclaim 1, wherein the target medical image analysis task is detection ofone or more anatomical landmarks in the input medical image, and theestimated output image is one of a mask image in which only locations ofthe one or more anatomical landmarks have non-zero pixel or voxel valuesor an image with a Gaussian-like circle defined surrounding locations ofthe one or more anatomical landmarks.
 3. The method of claim 1, whereinthe target medical image analysis task is detection of an anatomy ofinterest in the input medical image, and the estimated output image is amask image in which only pixels or voxels located within a bounding boxof the anatomy of interest have non-zero values.
 4. The method of claim1, wherein the target medical image analysis task is segmentation of oneor more anatomies of interest in the input medical image, and theestimated output image is one of a mask image in which only pixels orvoxels located within boundaries of the one or more anatomies ofinterest have non-zero values or an image with a Gaussian-like banddefined surrounding boundaries of the one or more anatomies of interest.5. The method of claim 1, wherein the target medical image analysis taskis lesion detection, segmentation, and characterization, and theestimated output image is a multi-label mask image in which only pixelsor voxels within lesion boundaries of one or more lesions have non-zerovalues assigned to each of the one or more lesions corresponding to alesion type for each lesion.
 6. The method of claim 1, wherein thetarget medical image analysis task is an image denoising task, and theestimated output image is a reduced noise image of the input medicalimage.
 7. The method of claim 1, wherein the input medical image is amedical image in a source domain, the target medical image analysis taskis cross-domain image synthesis, and the estimated output image is asynthesized medical image in a target domain corresponding the inputmedical image.
 8. The method of claim 1, wherein receiving the inputmedical image includes receiving the input medical image in a pair ofinput medical images acquired using different imaging modalities, thetarget medical image analysis task is registration of the pair of inputmedical images, and the estimated output image is a deformation fieldthat provides the registration between the pair of input medical images.9. The method of claim 1, wherein receiving the input medical imageincludes receiving the input medical image in a set of input medicalimages, the target medical image analysis task is a quantitativeparametric mapping task, and the estimated output image is a set ofquantitative parameters that generate the set of input medical imagesgiven a pointwise generative model.
 10. The method of claim 1, furthercomprising, in a training stage prior to receiving the input medicalimage of the patient: defining a type of output image that provides aresult of the target medical image analysis task; receiving a pluralityof input training images; receiving or generating corresponding outputtraining images for the plurality of input training images, resulting ina training set of paired input and output training images; and trainingthe DI2IN that uses the CRF energy function by learning weightparameters of the deep learning network that models the unary andpairwise terms of the CRF energy function that result in a maximumlikelihood for paired input and output training images over the trainingset of paired input and output training images.
 11. The method of claim1, wherein automatically generating the output image that provides theresult of the target medical image analysis task on the input medicalimage using the trained deep image-to-image network (DI2IN) comprises:maximizing a likelihood of the CRF energy function given the inputmedical image and a set of learned weight parameters of the trained deeplearning network, wherein the trained deep learning network calculatesthe unary and pairwise terms of the CRF energy function based on theinput medical image, the estimated output image, and the set of learnedweight parameters of the trained deep learning network.
 12. The methodof claim 1, wherein the respective output image generated for each ofthe plurality of reduced resolution images of the input medical imagedefines a region of interest that is cropped from an image at a higherresolution.
 13. An apparatus for automatically performing a medicalimage analysis task on a medical image of a patient, comprising: meansfor receiving an input medical image of a patient; and means forautomatically generating an output image that provides a result of atarget medical image analysis task on the input medical image using atrained deep image-to-image network (DI2IN), wherein the DI2IN uses aconditional random field (CRF) energy function to estimate the outputimage based on the input medical image and uses a trained deep learningnetwork to model unary and pairwise terms of the CRF energy function,wherein the means for automatically generating the output image thatprovides the result of the target medical image analysis task on theinput medical image using the DI2IN comprises: means for generating animage pyramid with a plurality of reduced resolution images of the inputmedical image at an original resolution; means for generating arespective output image that provides a result of the target medicalimage analysis task on each of the reduced resolution images of theinput medical image using a sequence of trained DI2INs; means fordividing the input medical image at the original resolution into aplurality of parts; means for generating a respective output image thatprovides a result of the target medical image analysis task on each ofthe plurality of parts of the original resolution input medical imageusing a respective trained DI2IN for each of the plurality of parts; andmeans for aggregating the output images that provide the results of thetarget medical image analysis task on each of the plurality of parts togenerate a final output image that provides the result of the targetmedical image analysis task on the input medical image.
 14. Theapparatus of claim 13, wherein the target medical image analysis task isone of anatomic landmark detection, anatomic structure detection,anatomic structure segmentation, lesion detection, segmentation orcharacterization, image denoising, cross-domain image synthesis,cross-modality image registration, or quantitative parameter mapping.15. The apparatus of claim 13, further comprising means for training theDI2IN that uses the CRF energy function comprising: means for defining atype of output image that provides a result of the target medical imageanalysis task; means for receiving a plurality of input training images;means for generating corresponding output training images for theplurality of input training images, resulting in a training set ofpaired input and output training images; and means for training theDI2IN that uses the CRF energy function by learning weight parameters ofthe deep learning network that models the unary and pairwise terms ofthe CRF energy function that result in a maximum likelihood for pairedinput and output training images over the training set of paired inputand output training images.
 16. The apparatus of claim 13, wherein themeans for automatically generating the output image that provides theresult of the target medical image analysis task on the input medicalimage using the trained deep image-to-image network (DI2IN) comprises:means for maximizing a likelihood of the CRF energy function given theinput medical image and a set of learned weight parameters of thetrained deep learning network, wherein the trained deep learning networkcalculates the unary and pairwise terms of the CRF energy function basedon the input medical image, the estimated output image, and the set oflearned weight parameters of the trained deep learning network.
 17. Theapparatus of claim 13, wherein the respective output image generated foreach of the plurality of reduced resolution images of the input medicalimage defines a region of interest that is cropped from an image at ahigher resolution.
 18. A non-transitory computer readable medium storingcomputer program instructions for automatically performing a medicalimage analysis task on a medical image of a patient, the computerprogram instructions when executed by a processor cause the processor toperform operations comprising: receiving an input medical image of apatient; and automatically generating an output image that provides aresult of a target medical image analysis task on the input medicalimage using a trained deep image-to-image network (DI2IN), wherein theDI2IN uses a conditional random field (CRF) energy function to estimatethe output image based on the input medical image and uses a traineddeep learning network to model unary and pairwise terms of the CRFenergy function, wherein automatically generating the output image thatprovides the result of the target medical image analysis task on theinput medical image using the DI2IN comprises: generating an imagepyramid with a plurality of reduced resolution images of the inputmedical image at an original resolution; generating a respective outputimage that provides a result of the target medical image analysis taskon each of the reduced resolution images of the input medical imageusing a sequence of trained DI2INs; dividing the input medical image atthe original resolution into a plurality of parts; generating arespective output image that provides a result of the target medicalimage analysis task on each of the plurality of parts of the originalresolution input medical image using a respective trained DI2IN for eachof the plurality of parts; and aggregating the output images thatprovide the results of the target medical image analysis task on each ofthe plurality of parts to generate a final output image that providesthe result of the target medical image analysis task on the inputmedical image.
 19. The non-transitory computer readable medium of claim18, wherein the target medical image analysis task is one of anatomiclandmark detection, anatomic structure detection, anatomic structuresegmentation, lesion detection, segmentation or characterization, imagedenoising, cross-domain image synthesis, cross-modality imageregistration, or quantitative parameter mapping.
 20. The non-transitorycomputer readable medium of claim 18, wherein the operations furthercomprise, in a training stage prior to receiving the input medical imageof the patient: defining a type of output image that provides a resultof the target medical image analysis task; receiving a plurality ofinput training images; receiving or generating corresponding outputtraining images for the plurality of input training images, resulting ina training set of paired input and output training images; and trainingthe DI2IN that uses the CRF energy function by learning weightparameters of the deep learning network that models the unary andpairwise terms of the CRF energy function that result in a maximumlikelihood for paired input and output training images over the trainingset of paired input and output training images.
 21. The non-transitorycomputer readable medium of claim 18, wherein automatically generatingthe output image that provides the result of the target medical imageanalysis task on the input medical image using the trained deepimage-to-image network (DI2IN) comprises: maximizing a likelihood of theCRF energy function given the input medical image and a set of learnedweight parameters of the trained deep learning network, wherein thetrained deep learning network calculates the unary and pairwise terms ofthe CRF energy function based on the input medical image, the estimatedoutput image, and the set of learned weight parameters of the traineddeep learning network.
 22. The non-transitory computer readable mediumof claim 18, wherein the respective output image generated for each ofthe plurality of reduced resolution images of the input medical imagedefines a region of interest that is cropped from an image at a higherresolution.